A numerical model is developed for studying the transport of bacterial facilitated contaminants in a coupled fracture-matrix system. The contaminants and bacteria are assumed to sorb onto the fracture surface, the contaminants are assumed to diffuse into the rock-matrix. Bacteria are assumed not to diffuse into the rock-matrix. The sorption of the contaminants onto the mobile and immobile bacteria within the fracture is assumed to be linear. The governing equations describing the bacterial transport and contaminant transport along the fracture as well as rock-matrix are coupled with each other. The coupled non-linear equations are solved numerically with fully implicit finite difference method. Constant concentration is assumed at the inlet of the fracture for both contaminants and bacteria. A varying grid is adopted at the fracture and rock-matrix interface to capture the flux transfer to ensure fluid mass transfer. Sensitivity analysis is performed to investigate the effects of various bacterial transport properties on the contaminant concentration in the fracture-matrix coupled system. Results suggest that for the contaminant and bacterial transport parameters that have been analysed, the bacterial concentration increases nearer to the fracture inlet due to consumption of contaminant substrate and consequently the contaminant concentration drastically reduces at the in the vicinity of fracture inlet. When the bacterial cells completely decay, the dead bacterial cells release the contaminants into the aqueous phase resulting in instantaneous increase in the contaminant concentration further away from the fracture inlet. For low matrix porosity and high half fracture aperture, bacterial concentration is consistent for a large portion of the fracture. There is significant bacterial concentration throughout the length of the fracture when the sorption coefficient of bacteria on the fracture wall surface is very low. When specific growth rate of bacteria is very high, an exponential growth pattern is observed nearer to the fracture inlet. © 2011 Elsevier B.V.